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Sample GSM39896 Query DataSets for GSM39896
Status Public on Feb 21, 2005
Title Adrenal 1111
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Adrenal 1111
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24469.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2
UNF_VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 208 155 109 76 99 79 213 164 110 75 104 88 0 0 47 46 23 16 92 90 88 86 178 192 1.253 .798 .846 .837 .884 1.798 52 286 .759 .73 80 1550 7900 42 50 35 43 0 141 69 72 .725 149 80 1.378 .769 -.463 -.379 -.463
2 180 95 110 73 70 22 189 95 112 74 79 22 0 0 40 22 24 16 82 65 73 28 92 101 3.182 .314 .278 .37 .37 2.18 52 244 .298 .45 80 1690 7900 42 50 49 57 0 86 66 20 .286 86 20 3.5 .253 -1.807 -1.982 -1.807
3 564 1105 108 79 456 1026 620 1201 110 82 512 1122 0 0 215 505 23 17 100 100 100 98 1482 1634 .444 2.25 2.191 2.134 2.261 1.523 80 347 2.325 .96 100 1840 7900 41 51 63 73 0 1005 72 933 2.045 1092 1020 .489 1.992 1.032 .994 1.032
4 1393 4018 107 84 1286 3934 1388 3868 110 85 1281 3784 0 0 818 2468 25 18 98 100 98 100 5220 5065 .327 3.059 2.954 3.172 3.007 1.65 80 365 3.115 .97 100 1980 7900 41 51 77 87 0 3653 76 3576 2.781 3516 3440 .36 2.685 1.476 1.425 1.476
5 254 352 112 83 142 269 256 367 113 86 144 284 0 0 92 127 26 19 90 100 78 100 411 428 .528 1.894 1.972 2.137 1.877 1.807 52 274 1.702 .9 80 2120 7900 42 50 92 100 0 320 75 245 1.722 334 258 .581 1.793 .784 .842 .784
6 178 154 116 87 62 67 172 160 118 89 56 73 0 0 51 42 26 16 75 84 56 78 129 129 .925 1.081 1.304 1.334 1.241 2.421 32 218 .789 .65 70 2270 7900 42 49 107 114 0 140 79 61 .982 145 66 1.018 1.185 -.026 .245 -.026
7 327 396 118 87 209 309 349 423 121 87 231 336 0 0 100 137 28 21 94 94 90 92 518 567 .676 1.478 1.455 1.392 1.412 1.653 52 240 1.418 .91 80 2410 7900 42 50 121 129 0 360 79 281 1.344 385 305 .744 1.322 .427 .403 .427
8 1180 3351 119 82 1061 3269 1275 3344 122 85 1156 3262 0 0 633 2116 44 21 97 100 91 100 4330 4418 .325 3.081 2.822 3.012 3.135 1.629 80 403 3.245 .96 100 2560 7900 41 51 135 145 0 3046 75 2972 2.801 3040 2965 .357 2.565 1.486 1.359 1.486
9 503 2029 117 85 386 1944 526 2084 117 87 409 1999 0 0 158 768 24 18 100 100 100 100 2330 2408 .199 5.036 4.888 5.074 5.333 1.63 52 277 5.337 .92 80 2710 7900 42 50 151 159 0 1845 77 1767 4.578 1895 1817 .218 4.443 2.195 2.152 2.195
10 193 202 116 85 77 117 202 212 118 86 86 127 0 0 50 61 29 20 84 90 71 84 194 213 .658 1.519 1.477 1.32 1.444 2.024 32 198 1.062 .46 70 2860 7900 42 49 166 173 0 184 77 106 1.381 193 115 .724 1.342 .466 .425 .466
11 503 831 111 85 392 746 495 832 115 87 384 747 0 0 245 432 27 18 98 100 96 100 1138 1131 .525 1.903 1.945 1.875 1.889 1.388 52 322 1.905 .94 90 2990 7900 41 50 178 187 0 755 77 678 1.73 756 679 .578 1.768 .791 .822 .791
12 695 562 111 85 584 477 720 564 113 86 609 479 0 0 208 143 25 17 98 100 98 100 1061 1088 1.224 .817 .787 .84 .828 1.311 52 301 .773 .95 90 3140 7900 41 50 193 202 0 511 77 434 .743 513 435 1.347 .715 -.429 -.484 -.429
13 380 758 115 82 265 676 394 839 272 108 279 757 0 0 146 368 1058 167 0 86 0 73 941 1036 .392 2.551 2.713 2.389 2.417 1.553 52 323 .17 .59 90 3280 7890 40 49 207 216 0 689 75 615 2.319 763 688 .431 2.467 1.214 1.303 1.214
14 203 288 113 86 90 202 205 292 293 117 92 206 0 0 53 94 1150 180 0 63 0 3 292 298 .446 2.244 2.239 2.215 2.133 1.802 52 271 2.193 .8 80 3440 7890 41 49 224 232 0 262 78 184 2.04 265 187 .49 2.036 1.029 1.025 1.029
15 2072 3381 114 86 1958 3295 2129 3674 116 88 2015 3588 0 0 983 1742 27 19 98 100 98 100 5253 5603 .594 1.683 1.781 1.649 1.678 1.497 80 405 1.732 .97 100 3580 7890 40 50 237 247 0 3074 78 2995 1.53 3340 3262 .654 1.619 .613 .695 .613
16 619 3032 115 86 504 2946 629 3247 117 87 514 3161 0 0 157 823 27 17 98 100 98 100 3450 3675 .171 5.845 6.15 5.819 5.994 1.283 52 292 6.006 .95 90 3730 7890 40 49 252 261 0 2756 78 2678 5.314 2952 2874 .188 5.591 2.41 2.483 2.41
17 152 125 112 83 40 42 157 120 114 84 45 37 0 0 42 29 23 17 75 81 46 53 82 82 .952 1.05 .822 .946 .918 2.941 32 220 .661 .41 70 3870 7900 42 49 267 274 0 114 75 38 .955 109 34 1.048 .747 -.067 -.42 -.067
18 185 121 121 84 64 37 186 122 121 86 65 38 0 0 40 14 24 19 83 83 75 50 101 103 1.73 .578 .585 .582 .51 2.41 12 104 .377 .46 50 4020 7900 43 48 283 288 0 110 76 34 .526 111 35 1.903 .531 -.928 -.912 -.928
19 452 538 120 93 332 445 459 563 122 94 339 470 0 0 200 236 30 20 93 90 87 90 777 809 .746 1.34 1.386 1.225 1.389 1.801 32 156 1.312 .94 60 4160 7900 43 49 297 303 0 489 85 405 1.219 512 427 .821 1.26 .285 .334 .285
20 171 134 117 94 54 40 175 139 120 96 58 45 0 0 50 31 27 18 81 81 56 68 94 103 1.35 .741 .776 .696 .676 1.94 32 201 .5 .49 70 4310 7890 41 48 311 318 0 122 85 36 .673 126 41 1.485 .705 -.57 -.504 -.57

Total number of rows: 43008

Table truncated, full table size 9137 Kbytes.




Supplementary data files not provided
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